A leading Fifa official has been accused by Swiss magistrates of receiving bribes in the course of an investigation into the collapse of ISMM, the former marketing partner of world football's governing body.

Nicolás Leoz, a Fifa executive committee member and long-serving president of Conmebol, the South American football confederation, is said to have been sent bribes totalling SFr211,625 (£90,000) in two separate payments in January and May 2000.

The money was paid by an entity linked to ISMM, the collapse of which in 2001 left a major hole in Fifa's finances. When contacted by the Guardian Leoz expressed surprise and said he had no connection with the companies in question.

The claim comes in a Swiss investigating magistrate's report relating to the collapse of ISMM. Prior to its bankruptcy, ISMM looked after distribution of television rights for the 2002 and 2006 World Cups, excluding Europe and the US, on Fifa's behalf, while the related company ISL Worldwide administered global distribution of marketing licences for the two competitions.

The allegation is set to rock football's rulers at a time when the integrity of the sport's business dealings is under scrutiny at home and abroad.

The legal document, which the Guardian has seen, refers to payments made between 1999 and early 2001 from a Liechtenstein bank account in the name of Sunbow SA, an entity said to have been founded in 1997 in the offshore finance centre of the British Virgin Islands.

The document asserts that Sunbow was "100 per cent held by the Nunca foundation, which in turn can be characterised as a financial/commercial unit of ISMM AG". It says that Nunca gave directions for Sunbow to be dissolved in May 2001.

Focusing on SFr18.2m (£7.75m) deployed for "payments for the acquisition of rights", the document states that these payments "are inducements (bribes) to third parties having a direct or indirect relationship to agreements negotiated by the ISMM group".

Of the payments to Leoz - dated January 20 and May 4 2000 - the Swiss investigators say that the "qualification of these payments as bribes is based on the statements made by Jean-Marie Weber himself ... and statements made by Hans-Peter Weber".

These two are former ISMM/ISL executives who were among six individuals being investigated by the Office of the Investigating Magistrate in the Swiss canton of Zug on charges including fraud, fraudulent bankruptcy and damage to creditors' interests by reduction of assets. The results of the investigation have been passed to local prosecutors, although court proceedings have not yet taken place. All deny the accusations.

Most of the payments are not believed to be football-related. It has been reported that the ISL liquidator has said no Swiss nationals were among football officials who took bribes from ISL, which would leave Fifa's president, Sepp Blatter, in the clear. ISMM's collapse, which came after it agreed to pay the ATP men's tennis tour $1.2bn (then about £800,000) for its media rights, shook Fifa during the final preparations for the 2002 World Cup in Japan and South Korea. It also sparked allegations that football officials had taken bribes from ISL.

Another of the former ISMM executives under investigation, Christoph Malms, is quoted in the legal document as saying: "The payment of inducements to reputable personalities in sport for the promotion of sport policy and financial objectives originates from the 1970s, when sport became a financial driver.

"I was confronted with the fact that ISL had been engaging in such practices since the time of its foundation..." He went on to say that he disapproved of the arrangements: "Upon my repeated urgings to suspend the payment of inducements, it was made clear to me by Jean-Marie Weber ... that this practice had led to commitments which were still in place."

He added: "The Nunca topic which you raise relates to accruals to personalities and decision-makers in world sport who were involved in the new acquisition or extension of worldwide marketing rights which were acquired by the ISL group."

Weber is said to have characterised the payments as "commissions, fees" paid "in parallel with the purchase or sale of rights". He said such payments were standard practice and necessary in the business. However, the document argues that "finder fees" also referred to by Mr Weber "can only be described in plain language as bribery".

It says it is for "the adjudicating court to decide what sum must ultimately be qualified as bribery". Such payments would not have been criminal under Swiss law. Separately, Hans-Peter Weber, along with another of the individuals under investigation, is said to have "answered in the negative to the question of whether Sunbow AG belonged to the ISMM group".

A statement obtained from Conmebol in response to the Guardian's questions about the payments said that: "Nicolás Leoz in 50 years has never had any problem of any kind. He is very surprised by your questions. Conmebol has never been in contact with the enterprises mentioned in these questions." Fifa said it was not served with a copy of the document and therefore could not comment.

It appears that some of the money might have been repaid. The document notes that on March 17 2004, "the account of ISL Worldwide in liquidation was credited with SFr2.5m".

Disclosure of the bribe allegations comes at a delicate moment in football politics, with contests for the presidencies of both Uefa and Fifa due next year.